A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants

Bethany Dearlove, Eric Lewitus, Hongjun Bai, Yifan Li, Daniel B. Reeves, M. Gordon Joyce, Paul T. Scott, Mihret F. Amare, Sandhya Vasan, Nelson L. Michael, Kayvon Modjarrad*, Morgane Rolland*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

147 Scopus citations


The magnitude of the COVID-19 pandemic underscores the urgency for a safe and effective vaccine. Many vaccine candidates focus on the Spike protein, as it is targeted by neutralizing antibodies and plays a key role in viral entry. Here we investigate the diversity seen in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences and compare it to the sequence on which most vaccine candidates are based. Using 18,514 sequences, we perform phylogenetic, population genetics, and structural bioinformatics analyses. We find limited diversity across SARS-CoV-2 genomes: Only 11 sites show polymorphisms in >5% of sequences; yet two mutations, including the D614G mutation in Spike, have already become consensus. Because SARS-CoV-2 is being transmitted more rapidly than it evolves, the viral population is becoming more homogeneous, with a median of seven nucleotide substitutions between genomes. There is evidence of purifying selection but little evidence of diversifying selection, with substitution rates comparable across structural versus nonstructural genes. Finally, the Wuhan-Hu-1 reference sequence for the Spike protein, which is the basis for different vaccine candidates, matches optimized vaccine inserts, being identical to an ancestral sequence and one mutation away from the consensus. While the rapid spread of the D614G mutation warrants further study, our results indicate that drift and bottleneck events can explain the minimal diversity found among SARS-CoV-2 sequences. These findings suggest that a single vaccine candidate should be efficacious against currently circulating lineages.

Original languageEnglish
Pages (from-to)23652-23662
Number of pages11
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number38
StatePublished - 22 Sep 2020
Externally publishedYes


  • Evolution
  • SARS-CoV-2
  • Vaccine


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